Switching between the mining dim and overworld makes your XP disappear and on certain occasions it makes the game crash when picking up an XP orb (player is ticking crash) the only fix to get back into the world is to use NBTExplorer or something that gives you the ability to change XYZ Position of the player so you dont pick up the xp.
Not sure what really causes it but that the instance i noticed when it occurs.

I'm not sure if this is related or not, but it seems it might be. I think the experience capsule itself is the cause of your issue entirely. Just today I crafted the item to make those seeds, and my world is now crashing over and over immediately on join with a 'ticking player' error and this happened right after I picked up my first xp orb while holding the capsule. I'm not sure if I should create a new issue for this or just comment on this one. My levels were still visible, I have not visited any mining dimension, and have a similar crash.

Thanks to CloneBoss42 on the discord, I found a relevant issue: BlakeBr0/MysticalAgriculture#477

Make sure to not have armor/weapons with mending when you try and use the experience capsules from MA.

edit: since i also noticed issue #187 it could also be a problem with having an experience capsule from Mystical which casues this.
(Having levels reset by moving between dimensions and then picking up XP since it goes into the capsule and not the player therefor game is confused and just crashes)